MHC class I genes encoding transplantation antigens are ubiquitously expressed, although their level of expression varies among tissues. Analysis of the 5' flanking DNA sequences of a swine class I gene has demonstrated that in addition to the canonical promoter, this region contains a series of negative and positive regulatory elements. One of the regulatory elements (RE-140) associated with this gene consists of overlapping negative and positive elements. Introduction into transgenic mice of a series of nested deletions containing a common 3' terminus, but differing in the extent of 5' flanking regulatory sequences, reveals that this complex regulatory element functions in a tissue specific manner, such that the enhancer activity predominates in lymphoid tissues, but not in non-lymphoid tissues. Another negative regulatory element, RE-105, has been identified which is distinct from RE-140 in both sequence and function. In transgenic animals, RE105 functions as a silencer in all tissues examined. The silencer component of RE-140 has been shown to have striking similarities to the yeast mating type repression system. A moderate DNA sequence homology exists between the yeast and mammalian operators. Mammalian factors bind to the yeast alpha2 operator and also specifically interact with a yeast alpha2-binding protein. Further, the yeast alpha2 operator functions as a silencer element in mammalian cells when placed upstream of a MHC class I promoter. All of the functionally identified regulatory elements are associated with trans acting factors. RE-140 DNA forms distinct enhancer and silencer associated complexes with cellular factors. Each consists of at least two distinct factors. Analysis of binding activity from a variety of cell lines and tissues reveals that RE-140 enhancer binding activity is present in all extracts, independent of the level of class I expression. The level of RE-140 silencer binding activity is inversely proportion to the level of class I gene expression. These studies have led to the proposal that class I genes are negatively regulated.